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- PDB-4wit: TMEM16 lipid scramblase in crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 4wit
TitleTMEM16 lipid scramblase in crystal form 2
ComponentsPredicted protein
KeywordsLIPID TRANSPORT / membrane protein / calcium activation / transport protein
Function / homology: / Alpha-beta plait domain in TMEM16 lipid scramblase / Anoctamin / : / Calcium-activated chloride channel / identical protein binding / membrane / metal ion binding / Plasma membrane channel protein
Function and homology information
Biological speciesNectria haematococca (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 Å
AuthorsDutzler, R. / Brunner, J.D. / Lim, N.K. / Schenck, S.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
European Research Council339116-AnoBest Switzerland
SNSFNCCR TransCure Switzerland
CitationJournal: Nature / Year: 2014
Title: X-ray structure of a calcium-activated TMEM16 lipid scramblase.
Authors: Brunner, J.D. / Lim, N.K. / Schenck, S. / Duerst, A. / Dutzler, R.
History
DepositionSep 26, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Database references
Revision 1.3May 8, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Predicted protein
B: Predicted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,5606
Polymers166,4002
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9760 Å2
ΔGint-101 kcal/mol
Surface area63570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.940, 127.240, 180.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Predicted protein


Mass: 83200.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nectria haematococca (fungus) / Strain: 77-13-4 / ATCC MYA-4622 / FGSC 9596 / MPVI / Gene: NECHADRAFT_66456 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: C7Z7K1
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.99 Å3/Da / Density % sol: 69.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 21-23% PEG400, 50 mM HEPES pH 7.4, 100 mM Ammonium sulfate
PH range: 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 36952 / % possible obs: 98.9 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 20
Reflection shellResolution: 3.4→3.5 Å / Redundancy: 8.6 % / Rmerge(I) obs: 1.47 / Mean I/σ(I) obs: 1.7 / % possible all: 87.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1760)refinement
XDSdata reduction
SHELXphasing
SHARPphasing
DMphasing
Omodel building
Cootmodel building
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.4→14.997 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2917 1596 4.38 %
Rwork0.2477 --
obs0.2498 36451 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→14.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10570 0 4 0 10574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210846
X-RAY DIFFRACTIONf_angle_d0.69914716
X-RAY DIFFRACTIONf_dihedral_angle_d15.163892
X-RAY DIFFRACTIONf_chiral_restr0.0261618
X-RAY DIFFRACTIONf_plane_restr0.0031864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4001-3.50850.3292610.32672880X-RAY DIFFRACTION89
3.5085-3.63220.3529940.30923216X-RAY DIFFRACTION100
3.6322-3.77540.38011320.30443164X-RAY DIFFRACTION100
3.7754-3.94430.37911570.29013141X-RAY DIFFRACTION100
3.9443-4.1480.35711520.27563166X-RAY DIFFRACTION100
4.148-4.40170.31011450.25383180X-RAY DIFFRACTION100
4.4017-4.73170.28321600.22583181X-RAY DIFFRACTION100
4.7317-5.18980.27341810.22113167X-RAY DIFFRACTION100
5.1898-5.90040.30331660.24813201X-RAY DIFFRACTION100
5.9004-7.2890.33621620.2763247X-RAY DIFFRACTION100
7.289-14.9970.23991860.21563312X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.68611.8099-0.65156.35860.16075.0438-1.07950.37410.0693-1.27280.60840.28390.389-0.41920.31531.5885-0.23890.07551.5505-0.15141.12118.792714.634-27.0853
24.83110.19861.29272.8014-0.09415.7452-0.68191.4958-0.9678-0.7560.7135-0.79070.05851.0802-0.10390.8977-0.04920.32180.8639-0.05921.22132.622611.2085-11.1362
34.05080.71840.51633.0034-0.28063.1326-0.03810.0607-0.4822-0.26980.063-0.24950.4154-0.41040.01260.59020.0020.02640.57930.02050.748118.83238.71847.8253
42.15570.6853-0.61413.6767-1.46884.9097-0.1556-0.009-0.7726-0.4227-0.0225-0.84811.5848-0.12560.06151.02720.05520.10910.6522-0.05881.271227.2992-4.80866.1159
51.19790.9359-0.12543.796-0.02811.033-0.1012-0.0750.2885-0.17690.1183-0.1375-0.3975-0.1662-0.06150.85960.1077-0.0690.98170.07251.234.195546.9879.3132
62.33221.4509-0.09924.4093-1.87382.0283-0.20030.09891.18690.27960.31410.6551-0.6744-0.3904-0.39560.82550.1573-0.06180.7631-0.00651.283524.674258.464613.2193
72.0915-0.0237-0.59433.02490.10693.11030.1901-0.49090.27470.6499-0.2214-0.0918-0.5925-0.0539-0.2220.798-0.0432-0.03440.8455-0.04610.867629.537746.837934.1136
80.27850.08780.30222.28241.52983.8036-0.12680.1589-0.0603-0.6839-0.1001-0.06440.5235-0.40360.1891.094-0.18440.08551.23670.13181.133719.005522.5713-6.0224
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 103 )
2X-RAY DIFFRACTION2chain 'A' and (resid 104 through 211 )
3X-RAY DIFFRACTION3chain 'A' and (resid 212 through 391 )
4X-RAY DIFFRACTION4chain 'A' and (resid 392 through 558 )
5X-RAY DIFFRACTION5chain 'A' and (resid 559 through 719 )
6X-RAY DIFFRACTION6chain 'B' and (resid 19 through 245 )
7X-RAY DIFFRACTION7chain 'B' and (resid 246 through 558 )
8X-RAY DIFFRACTION8chain 'B' and (resid 559 through 719 )

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